Starting phenix.real_space_refine on Thu Dec 7 20:22:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkg_17738/12_2023/8pkg_17738.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkg_17738/12_2023/8pkg_17738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkg_17738/12_2023/8pkg_17738.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkg_17738/12_2023/8pkg_17738.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkg_17738/12_2023/8pkg_17738.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkg_17738/12_2023/8pkg_17738.pdb" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2796 2.51 5 N 708 2.21 5 O 804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C ARG 103": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 103": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 103": "NH1" <-> "NH2" Residue "F ARG 21": "NH1" <-> "NH2" Residue "F ARG 103": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4314 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "B" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "C" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "E" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "F" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Time building chain proxies: 2.70, per 1000 atoms: 0.63 Number of scatterers: 4314 At special positions: 0 Unit cell: (78, 82.16, 46.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 804 8.00 N 708 7.00 C 2796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 755.8 milliseconds 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1044 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 45.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 26 removed outlier: 6.331A pdb=" N ALA A 25 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA B 25 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA C 25 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA D 25 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA E 25 " --> pdb=" O ILE F 26 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 29 through 34 Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 65 removed outlier: 6.566A pdb=" N THR A 60 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N GLU B 63 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLU A 62 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL B 65 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N PHE A 64 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR B 60 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N GLU C 63 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLU B 62 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL C 65 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N PHE B 64 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR C 60 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N GLU D 63 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLU C 62 " --> pdb=" O GLU D 63 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL D 65 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N PHE C 64 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR D 60 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N GLU E 63 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLU D 62 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL E 65 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N PHE D 64 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR E 60 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N GLU F 63 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLU E 62 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL F 65 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N PHE E 64 " --> pdb=" O VAL F 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 71 through 80 removed outlier: 6.759A pdb=" N THR A 75 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS B 76 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER A 77 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR B 78 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR B 75 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS C 76 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER B 77 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR C 78 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR C 75 " --> pdb=" O ASP D 74 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS D 76 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER C 77 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR D 78 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR D 75 " --> pdb=" O ASP E 74 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS E 76 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER D 77 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR E 78 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR E 75 " --> pdb=" O ASP F 74 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LYS F 76 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER E 77 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR F 78 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 92 through 99 removed outlier: 6.478A pdb=" N VAL A 93 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N THR B 96 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE A 95 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASN B 98 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA A 97 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL B 93 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N THR C 96 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE B 95 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASN C 98 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA B 97 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL C 93 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N THR D 96 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE C 95 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASN D 98 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA C 97 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL D 93 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N THR E 96 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE D 95 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASN E 98 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA D 97 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL E 93 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N THR F 96 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE E 95 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASN F 98 " --> pdb=" O PHE E 95 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA E 97 " --> pdb=" O ASN F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 104 through 106 removed outlier: 6.800A pdb=" N TYR A 105 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR B 105 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR C 105 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR D 105 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR E 105 " --> pdb=" O THR F 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AB1, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'A' and resid 118 through 122 removed outlier: 5.720A pdb=" N THR A 118 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL B 121 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA A 120 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N THR B 118 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL C 121 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA B 120 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N THR C 118 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL D 121 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA C 120 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N THR D 118 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL E 121 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA D 120 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N THR E 118 " --> pdb=" O THR F 119 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL F 121 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA E 120 " --> pdb=" O VAL F 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 90 hydrogen bonds defined for protein. 270 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 778 1.33 - 1.45: 1124 1.45 - 1.57: 2502 1.57 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 4416 Sorted by residual: bond pdb=" N SER C 85 " pdb=" CA SER C 85 " ideal model delta sigma weight residual 1.457 1.491 -0.034 9.10e-03 1.21e+04 1.40e+01 bond pdb=" N SER B 85 " pdb=" CA SER B 85 " ideal model delta sigma weight residual 1.457 1.490 -0.034 9.10e-03 1.21e+04 1.38e+01 bond pdb=" N SER A 85 " pdb=" CA SER A 85 " ideal model delta sigma weight residual 1.457 1.490 -0.034 9.10e-03 1.21e+04 1.37e+01 bond pdb=" N SER D 85 " pdb=" CA SER D 85 " ideal model delta sigma weight residual 1.457 1.490 -0.034 9.10e-03 1.21e+04 1.37e+01 bond pdb=" N SER E 85 " pdb=" CA SER E 85 " ideal model delta sigma weight residual 1.457 1.490 -0.034 9.10e-03 1.21e+04 1.36e+01 ... (remaining 4411 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.33: 197 106.33 - 113.31: 2336 113.31 - 120.29: 2068 120.29 - 127.28: 1369 127.28 - 134.26: 36 Bond angle restraints: 6006 Sorted by residual: angle pdb=" CA SER F 85 " pdb=" C SER F 85 " pdb=" N PRO F 86 " ideal model delta sigma weight residual 118.16 121.70 -3.54 7.00e-01 2.04e+00 2.56e+01 angle pdb=" CA SER C 85 " pdb=" C SER C 85 " pdb=" N PRO C 86 " ideal model delta sigma weight residual 118.16 121.70 -3.54 7.00e-01 2.04e+00 2.55e+01 angle pdb=" CA SER D 85 " pdb=" C SER D 85 " pdb=" N PRO D 86 " ideal model delta sigma weight residual 118.16 121.69 -3.53 7.00e-01 2.04e+00 2.55e+01 angle pdb=" CA SER A 85 " pdb=" C SER A 85 " pdb=" N PRO A 86 " ideal model delta sigma weight residual 118.16 121.69 -3.53 7.00e-01 2.04e+00 2.54e+01 angle pdb=" CA SER B 85 " pdb=" C SER B 85 " pdb=" N PRO B 86 " ideal model delta sigma weight residual 118.16 121.68 -3.52 7.00e-01 2.04e+00 2.53e+01 ... (remaining 6001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.01: 2166 8.01 - 16.02: 234 16.02 - 24.04: 114 24.04 - 32.05: 54 32.05 - 40.06: 36 Dihedral angle restraints: 2604 sinusoidal: 990 harmonic: 1614 Sorted by residual: dihedral pdb=" C TYR D 116 " pdb=" N TYR D 116 " pdb=" CA TYR D 116 " pdb=" CB TYR D 116 " ideal model delta harmonic sigma weight residual -122.60 -129.60 7.00 0 2.50e+00 1.60e-01 7.84e+00 dihedral pdb=" C TYR A 116 " pdb=" N TYR A 116 " pdb=" CA TYR A 116 " pdb=" CB TYR A 116 " ideal model delta harmonic sigma weight residual -122.60 -129.60 7.00 0 2.50e+00 1.60e-01 7.84e+00 dihedral pdb=" C TYR E 116 " pdb=" N TYR E 116 " pdb=" CA TYR E 116 " pdb=" CB TYR E 116 " ideal model delta harmonic sigma weight residual -122.60 -129.59 6.99 0 2.50e+00 1.60e-01 7.82e+00 ... (remaining 2601 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.058: 203 0.058 - 0.115: 247 0.115 - 0.173: 164 0.173 - 0.230: 76 0.230 - 0.287: 18 Chirality restraints: 708 Sorted by residual: chirality pdb=" CA ILE F 107 " pdb=" N ILE F 107 " pdb=" C ILE F 107 " pdb=" CB ILE F 107 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA ILE A 107 " pdb=" N ILE A 107 " pdb=" C ILE A 107 " pdb=" CB ILE A 107 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA ILE E 107 " pdb=" N ILE E 107 " pdb=" C ILE E 107 " pdb=" CB ILE E 107 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 705 not shown) Planarity restraints: 738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR F 114 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.32e+00 pdb=" C TYR F 114 " -0.043 2.00e-02 2.50e+03 pdb=" O TYR F 114 " 0.016 2.00e-02 2.50e+03 pdb=" N SER F 115 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 90 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.29e+00 pdb=" C HIS B 90 " -0.043 2.00e-02 2.50e+03 pdb=" O HIS B 90 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA B 91 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 90 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.29e+00 pdb=" C HIS D 90 " -0.043 2.00e-02 2.50e+03 pdb=" O HIS D 90 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA D 91 " 0.015 2.00e-02 2.50e+03 ... (remaining 735 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 1739 2.90 - 3.40: 3766 3.40 - 3.90: 7659 3.90 - 4.40: 8773 4.40 - 4.90: 16883 Nonbonded interactions: 38820 Sorted by model distance: nonbonded pdb=" O ASN A 27 " pdb=" OH TYR B 69 " model vdw 2.394 2.440 nonbonded pdb=" O ASN B 27 " pdb=" OH TYR C 69 " model vdw 2.395 2.440 nonbonded pdb=" O ASN C 27 " pdb=" OH TYR D 69 " model vdw 2.395 2.440 nonbonded pdb=" O ASN D 27 " pdb=" OH TYR E 69 " model vdw 2.395 2.440 nonbonded pdb=" O ASN E 27 " pdb=" OH TYR F 69 " model vdw 2.395 2.440 ... (remaining 38815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.510 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.960 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.041 4416 Z= 0.848 Angle : 1.652 7.321 6006 Z= 1.222 Chirality : 0.117 0.287 708 Planarity : 0.007 0.034 738 Dihedral : 10.764 40.059 1560 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 0.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.30), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 79 HIS 0.006 0.002 HIS F 31 PHE 0.013 0.002 PHE E 64 TYR 0.007 0.002 TYR B 116 ARG 0.003 0.001 ARG F 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 0.489 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.9882 time to fit residues: 213.8896 Evaluate side-chains 125 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.671 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS C 88 HIS ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4416 Z= 0.270 Angle : 0.674 8.173 6006 Z= 0.360 Chirality : 0.053 0.191 708 Planarity : 0.005 0.033 738 Dihedral : 5.126 15.631 594 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.70 % Allowed : 20.51 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.30), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 79 HIS 0.004 0.001 HIS E 31 PHE 0.015 0.002 PHE F 87 TYR 0.027 0.002 TYR B 114 ARG 0.007 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 0.523 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 137 average time/residue: 0.9576 time to fit residues: 136.6530 Evaluate side-chains 119 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 0.506 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 0.4779 time to fit residues: 3.2246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS B 27 ASN ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4416 Z= 0.326 Angle : 0.664 4.944 6006 Z= 0.356 Chirality : 0.051 0.205 708 Planarity : 0.004 0.029 738 Dihedral : 5.319 16.440 594 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 6.62 % Allowed : 20.51 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 79 HIS 0.004 0.001 HIS F 31 PHE 0.014 0.002 PHE D 95 TYR 0.025 0.002 TYR C 114 ARG 0.005 0.001 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 114 time to evaluate : 0.472 Fit side-chains outliers start: 31 outliers final: 16 residues processed: 129 average time/residue: 1.1708 time to fit residues: 156.2218 Evaluate side-chains 120 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 0.504 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 8 residues processed: 9 average time/residue: 0.2850 time to fit residues: 3.5262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4416 Z= 0.222 Angle : 0.602 6.753 6006 Z= 0.315 Chirality : 0.050 0.217 708 Planarity : 0.004 0.041 738 Dihedral : 5.136 16.874 594 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.06 % Allowed : 23.50 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.32), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 79 HIS 0.003 0.001 HIS E 31 PHE 0.012 0.002 PHE D 95 TYR 0.022 0.002 TYR C 114 ARG 0.008 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 0.523 Fit side-chains outliers start: 19 outliers final: 10 residues processed: 123 average time/residue: 1.1985 time to fit residues: 152.5921 Evaluate side-chains 111 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 0.519 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.1045 time to fit residues: 1.0938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 HIS ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 4416 Z= 0.444 Angle : 0.732 6.604 6006 Z= 0.384 Chirality : 0.052 0.137 708 Planarity : 0.005 0.054 738 Dihedral : 5.603 17.420 594 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.91 % Allowed : 23.93 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.32), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 79 HIS 0.006 0.001 HIS F 31 PHE 0.014 0.002 PHE A 87 TYR 0.021 0.002 TYR C 114 ARG 0.013 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 103 time to evaluate : 0.522 Fit side-chains outliers start: 23 outliers final: 11 residues processed: 116 average time/residue: 1.3453 time to fit residues: 160.8912 Evaluate side-chains 107 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.529 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.0898 time to fit residues: 1.0660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.5864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 4416 Z= 0.514 Angle : 0.763 8.801 6006 Z= 0.399 Chirality : 0.053 0.145 708 Planarity : 0.005 0.047 738 Dihedral : 5.826 18.327 594 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.56 % Allowed : 22.86 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.32), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 79 HIS 0.007 0.002 HIS F 31 PHE 0.012 0.002 PHE A 87 TYR 0.018 0.002 TYR C 114 ARG 0.007 0.001 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 0.530 Fit side-chains outliers start: 26 outliers final: 11 residues processed: 109 average time/residue: 1.3448 time to fit residues: 151.2630 Evaluate side-chains 101 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.546 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.0856 time to fit residues: 1.1188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.5946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4416 Z= 0.265 Angle : 0.645 8.647 6006 Z= 0.332 Chirality : 0.049 0.133 708 Planarity : 0.004 0.033 738 Dihedral : 5.422 18.081 594 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.06 % Allowed : 24.36 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.32), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 79 HIS 0.003 0.001 HIS D 31 PHE 0.009 0.002 PHE A 87 TYR 0.018 0.002 TYR C 114 ARG 0.007 0.001 ARG E 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 0.515 Fit side-chains outliers start: 19 outliers final: 10 residues processed: 110 average time/residue: 1.3387 time to fit residues: 152.1443 Evaluate side-chains 103 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.517 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.0428 time to fit residues: 0.7843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 40 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.6058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4416 Z= 0.283 Angle : 0.675 9.351 6006 Z= 0.342 Chirality : 0.050 0.132 708 Planarity : 0.005 0.041 738 Dihedral : 5.346 18.489 594 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.78 % Allowed : 26.92 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.33), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 79 HIS 0.003 0.001 HIS D 31 PHE 0.010 0.002 PHE A 87 TYR 0.018 0.002 TYR C 114 ARG 0.009 0.001 ARG E 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 0.483 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 106 average time/residue: 1.3210 time to fit residues: 144.5019 Evaluate side-chains 102 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.517 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.0406 time to fit residues: 0.7296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 49 optimal weight: 0.0060 chunk 42 optimal weight: 3.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.6147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 4416 Z= 0.392 Angle : 0.723 10.617 6006 Z= 0.371 Chirality : 0.051 0.145 708 Planarity : 0.005 0.040 738 Dihedral : 5.540 18.382 594 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.56 % Allowed : 26.92 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.32), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 79 HIS 0.005 0.001 HIS F 31 PHE 0.011 0.002 PHE A 87 TYR 0.018 0.002 TYR C 114 ARG 0.009 0.001 ARG E 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.506 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 102 average time/residue: 1.3170 time to fit residues: 138.6512 Evaluate side-chains 99 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.525 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.0430 time to fit residues: 0.7475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.6200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4416 Z= 0.274 Angle : 0.680 10.634 6006 Z= 0.343 Chirality : 0.050 0.157 708 Planarity : 0.005 0.046 738 Dihedral : 5.336 18.437 594 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.92 % Allowed : 27.78 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.33), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 79 HIS 0.003 0.001 HIS D 31 PHE 0.009 0.002 PHE A 87 TYR 0.017 0.002 TYR C 114 ARG 0.010 0.001 ARG E 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 0.479 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 9 residues processed: 102 average time/residue: 1.3721 time to fit residues: 144.2959 Evaluate side-chains 100 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 0.507 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 0.6636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 4.9990 chunk 5 optimal weight: 0.0770 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.140238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.110023 restraints weight = 6515.102| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.67 r_work: 0.3924 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.6225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4416 Z= 0.222 Angle : 0.671 10.977 6006 Z= 0.330 Chirality : 0.049 0.153 708 Planarity : 0.004 0.045 738 Dihedral : 5.119 18.173 594 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.92 % Allowed : 27.78 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.33), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 79 HIS 0.003 0.000 HIS D 31 PHE 0.008 0.001 PHE D 64 TYR 0.018 0.001 TYR C 114 ARG 0.010 0.001 ARG E 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2784.72 seconds wall clock time: 49 minutes 41.78 seconds (2981.78 seconds total)